method

nRowPerCand

nRowPerCand – number of realizations for
a multiSim reference system

...

... – parameters to classifiers

Details

Classifies genes according to distributional shape, by
comparing observed expression distributions to
a collection of references, which may be simulated
or evaluated theoretically.

The distList argument is important. It enumerates the
catalog of distributions for classification of gene
expression vectors by distributional shape. See the
HOWTO-edd vignette for information on how this list
is constructed and how it can be extended.

The tx argument specifies how the data are processed
for comparison to the reference catalog. This is
a function on a vector returning a vector, but the
input and the output need not have the same length.
The default value of tx is sort, which entails that
the order statistics are treated as multivariate data
for classification.

The refDist argument selects the type of reference
catalog. Options are 'multiSim', for which the
reference consists of nRowPerCand realizations of
each catalog entry, and 'theoretical', for which
the reference consists of one vector of quantiles
for each catalog entry.

The method argument selects the type of classifier.
It would be desirable to allow this to be a function,
but there is insufficient structure on classifier
argument and return value structure to permit this
at present; see the e1071 package for some work
on handling various classifiers programmatically
(e.g., tune).